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- PDB-1cmo: IMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR T... -

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Entry
Database: PDB / ID: 1cmo
TitleIMMUNOGLOBULIN MOTIF DNA-RECOGNITION AND HETERODIMERIZATION FOR THE PEBP2/CBF RUNT-DOMAIN
ComponentsPOLYOMAVIRUS ENHANCER BINDING PROTEIN 2
KeywordsTRANSCRIPTION / TRANSCRIPTION FACTOR / HEMATOPOIESIS / OSTEOGENESIS / IG-FOLD
Function / homology
Function and homology information


regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / myeloid leukocyte differentiation ...regulation of connective tissue replacement / peripheral nervous system neuron development / positive regulation of granulocyte differentiation / RUNX1 regulates transcription of genes involved in BCR signaling / SLC-mediated transport of organic cations / RUNX1 regulates transcription of genes involved in interleukin signaling / core-binding factor complex / RUNX1 regulates expression of components of tight junctions / positive regulation of CD8-positive, alpha-beta T cell differentiation / myeloid leukocyte differentiation / regulation of cardiac muscle cell proliferation / cardiac muscle tissue regeneration / negative regulation of CD4-positive, alpha-beta T cell differentiation / negative regulation of granulocyte differentiation / RUNX1 and FOXP3 control the development of regulatory T lymphocytes (Tregs) / positive regulation of extracellular matrix organization / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of plasminogen activation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / myeloid cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / Regulation of RUNX1 Expression and Activity / RUNX1 regulates transcription of genes involved in WNT signaling / RUNX1 regulates estrogen receptor mediated transcription / hematopoietic stem cell proliferation / RUNX1 interacts with co-factors whose precise effect on RUNX1 targets is not known / regulation of cell differentiation / hemopoiesis / positive regulation of collagen biosynthetic process / RUNX3 regulates p14-ARF / chondrocyte differentiation / positive regulation of interleukin-2 production / ossification / transcription corepressor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function / Pre-NOTCH Transcription and Translation / SARS-CoV-1 activates/modulates innate immune responses / transcription coactivator binding / Transcriptional regulation of granulopoiesis / neuron differentiation / positive regulation of angiogenesis / RUNX1 regulates transcription of genes involved in differentiation of HSCs / DNA-binding transcription activator activity, RNA polymerase II-specific / DNA-binding transcription factor binding / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription cis-regulatory region binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein heterodimerization activity / intracellular membrane-bounded organelle / calcium ion binding / regulation of transcription by RNA polymerase II / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / protein homodimerization activity / positive regulation of transcription by RNA polymerase II / DNA binding / nucleoplasm / ATP binding / nucleus
Similarity search - Function
Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily ...Runx, central domain superfamily / Acute myeloid leukemia 1 protein (AML1)/Runt / Runt domain / Runx, C-terminal domain / Runt-related transcription factor RUNX / Runt domain / Runx inhibition domain / Runt domain profile. / Immunoglobulin-like - #720 / p53/RUNT-type transcription factor, DNA-binding domain superfamily / p53-like transcription factor, DNA-binding / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Runt-related transcription factor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodSOLUTION NMR / HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING
AuthorsNagata, T. / Gupta, V. / Sorce, D. / Kim, W.Y. / Sali, A. / Chait, B.T. / Shigesada, K. / Ito, Y. / Werner, M.H.
CitationJournal: Nat.Struct.Biol. / Year: 1999
Title: Immunoglobulin motif DNA recognition and heterodimerization of the PEBP2/CBF Runt domain.
Authors: Nagata, T. / Gupta, V. / Sorce, D. / Kim, W.Y. / Sali, A. / Chait, B.T. / Shigesada, K. / Ito, Y. / Werner, M.H.
History
DepositionMay 11, 1999Deposition site: BNL / Processing site: RCSB
Revision 1.0Jan 5, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 16, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / pdbx_nmr_software ...database_2 / pdbx_nmr_software / pdbx_struct_assembly / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_nmr_software.name
Revision 1.4Dec 27, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

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Assembly

Deposited unit
A: POLYOMAVIRUS ENHANCER BINDING PROTEIN 2


Theoretical massNumber of molelcules
Total (without water)14,0091
Polymers14,0091
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
NMR ensembles
DataCriteria
Number of conformers (submitted / calculated)43 / 300structures with the least restraint violations
Representative

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Components

#1: Protein POLYOMAVIRUS ENHANCER BINDING PROTEIN 2 / ACUTE MYELOID LEUKEMIA 1 PROTEIN / AML1/OSF2 / PEBP2-ALPHA B


Mass: 14008.942 Da / Num. of mol.: 1 / Fragment: CORE-BINDING FACTOR ALPHA B SUBUNIT, RUNT DOMAIN / Mutation: C81S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PQE9 / Species (production host): Escherichia coli / Cellular location (production host): CYTOPLASM / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q01196

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Experimental details

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Experiment

ExperimentMethod: SOLUTION NMR
NMR experimentType: ALL STANDARD
NMR detailsText: ALL STANDARD

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Sample preparation

DetailsContents: 96% H2O/4% D2O
Sample conditionsIonic strength: 10mM / pH: 6.8 / Pressure: 1 atm / Temperature: 310 K
Crystal grow
*PLUS
Method: other / Details: NMR

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NMR measurement

NMR spectrometer
TypeManufacturerModelField strength (MHz)Spectrometer-ID
Bruker DMX500BrukerDMX5005001
Bruker DMX600BrukerDMX6006002

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Processing

NMR software
NameVersionDeveloperClassification
NMRPipestructure solution
PIPPstructure solution
STAPPstructure solution
X-PLORBRUNGERstructure solution
X-PLOR3.843BRUNGERrefinement
RefinementMethod: HYBRID DISTANCE GEOMETRY, SIMULATED ANNEALING / Software ordinal: 1
NMR ensembleConformer selection criteria: structures with the least restraint violations
Conformers calculated total number: 300 / Conformers submitted total number: 43

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